A certain Creator has always existed. Never created, but simply always... there.
Approximately 4,000,000,000 years prior to current events, the Creator started working. Orbs of dirt, gas, and water began forming, and shining lights were placed in the black darkness of space.
And there was one planet that the Creator put special attention into. Here, the Creator fashioned three round containers - these eventually broke apart, bringing forth three beings, all with the power of creation.
These three - Uxie, Mesprit, and Azelf - quickly knew of the imbalance with no direct rulers of time and space, so they set their powers to work: Dialga, who governs time, and Palkia, who governs space.
Not long after this, the Creator decided to set up a guardian of this planet. The titan Regigigas was formed, the first Pokémon to set foot on this planet. He pulled the continents into their current places, and they are there to this day.
The Creator noticed the titan's loneliness, and so came forth the ancients - Omanyte, Kabuto, Aerodactyl, Lileep, Anorith, Cranidos, Shieldon, Tirtouga, Archen, Tyrunt, and Amaura, as well as their evolutions. The Creator also fashioned Rayquaza, which simply lived up in the ozone layer all alone.
As the Creator was designing these Pokémon, the titan was building. Out of rocks, ice, and metal, Regigigas created three new titans - Regirock, Regice, and Registeel. These, along with their master, were simply intended to guard the planet, but the ancient Pokémon would have none of their immense power - and so they were locked up across the world, forever to rot.
But the ancients weren't done yet. They didn't want to be ruled; rather, they preferred to just do whatever they wanted.
And the Creator was not amused.
Before long, war raged. All the ancients, every last one, were turned into fossils and buried. The world was returned to emptiness. Until the Creator decided to start over some 3,000,000,000 years prior from current time.
For two billion years, all Pokémon in existence (minus the ancients) lived in peace, although the Creator was not heard from. Time and space lived in perfect harmony with no one really knowing about them.
But then the battles truly began. The master of water, Kyogre, and the master of land, Groudon, sought to expand their territories and, in their own minds, make the world better. At the same time, the ruler of time, Dialga, and ruler of space, Palkia, began to battle as they each thought the other was intruding upon their realms.
Space-time distortions occured everywhere. The waters flooded the land, but the land covered the water.
And then Rayquaza came down from the ozone layer of the world and, being the first to show this power, performed Mega Evolution, and defeated both Kyogre and Groudon, which were then put to sleep deep in the world. A barrier was finally placed between space and time - the reverse world (or the Distortion World as it is now known). Giratina guards this place.
Finally, peace had truly come. From then 'til now, there hasn't been any universe-rattling wars or battles. The Creator has been resting, awaiting the time already set - the time of revenge.
It is up to debate... until I explain it. I'm planning on having some guy explain most of the lore, and then there will likely be more that is left out, but will definitely be explained. At some point.
In that case, 4,000 years is a very short time between the creation of the world to present day. Using human history as a rough guide, that takes you back to 2,000 BC, at which point Stonehenge was probably finished, Egyptian civilisation was in full swing, and horses were tamed. Compare the invention of agriculture, at somewhere between 10 and 12,000 years ago.
I've just realised I'm assuming your present day is supposed to be the modern day, so, something to think about
Maybe the world is young! Besides, technology advanced quickly during the 2000 Years of Peace before the water/land and space/time battles began. They weren't totally up to date by then as Porygon wouldn't have existed, but fairly close.
Is there any reason why it has to be 4,000 years? If not, there's no real reason why you can't simply change the date. Good worldbuilding is about teasing out the problems and making changes to correct them. It's almost always better to correct a problem than it is to hope your readers either won't notice or will ignore it, because suspension of disbelief is a finite currency
You could still get away with a comparatively young world, since the Creator in this case is literally creating species from nothing. That lets you skip some billions of years of single-celled organisms very slowly becoming multicellular
I've established how the Battle Kukku from Sonic the Hedgehog are descended from the Chozo of Metroid, how Magnemite were once probes sent down to the Pokémon world to study it before The War that saw the Human race scattered on planets without any method of communications or getting back into space, eventually resulting in those memories lost and confused (Pokémon are the space guys, eh?) and their society turning into what is shown. And there's a perfectly good reason why the planet and Earth look similar...
Well ... depends what you call "lore". I'm not a huge fan of terms like "lore" or "fluff" ... I do have a working history and geography of the canon regions in my head, just so I can keep what references I do have to make in the story straight. I'm wary of the old J.K Rowling trap, so I've deliberately not given much in the way of concrete details in The Long Walk itself
I need to go deeper into lore in both my Sonic-based comics and Dragon Ball-based fanfic. In the comics, I need to explain where Mobians came from and why they're living on Earth beside the Earthlings, along with the history of the Helmest and Lanthanoids, both alien races (that are strikingly similar to Mobian species). And in the fanfic, world-building mostly.